Background The envelope glycoprotein of the human (HIV) and related simian (SIV) immunodeficiency virus are synthesized as gp160 precursors which are processed into two non-covalently associated glycoproteins: gp120 and gp41. The gp120 mediates viral entry into the host cell by binding to the cellular receptor CD4 and a chemokine coreceptor, both of which are located on the host cell surface. This binding induces conformational changes in the transmembrane gp41, which facilitates membrane fusion between the viral and host membranes. An understanding of these processes at the molecular level may lead to a direct means of inhibiting HIV infection. As HIV pg41, and the closely related SIV gp41, are heavily glycosylated transmembrane proteins determination of their high&#64979;resolution structures is a very difficult problem. In an incremental approach, we are studying the structure of (non-glycosylated) functional domains of gp41. The most important region of gp41 is the ectodomain region, located on the outer surface of the viral membrane, which directly mediates membrane fusion events. Both HIV and SIV gp41 ectodomains have been expressed in E.coli. For the SIV gp41, both the NMR and X-ray structures have been solved. Results High-resolution X-ray (Hyde/Wang) and NMR (Clore/Gronenborn/Caffrey) structures of the SIV gp41 ectodomain (e-gp41) have been determined. The structure determined by both methods is a rod-like trimer comprising three parallel N-terminal a-helices assembled as a coiled-coil in the center with three antiparallel C-terminal a-helices packed on the outside with highly flexible loops connecting the inner and outer helices. The loop region connecting the inner and outer helices, although not clearly resolved in the X-ray model, has been modeled in the NMR structure allowing the connectivity's between inner and outer helices to be established. This region appears responsible for the low solubility of the trimer at physiological pH values resulting in aggregate formation. Aggregates of e-gp4 are composed of between 7-70 trimers, which are associated by interactions at the interior of the aggregate involving the loop region. In the brains of HIV-1 infected patients diagnosed with dementia, HIV-1 gp41 accumulates as an extracellular aggregate. It is postulated that the high molecular aggregates of e-gp41 are responsible for HIV-associated neurological damage and dementia. Peptides from the C-terminal helix of e-gp41 inhibit fusion at nM concentrations. It has been proposed that the peptides bind to the exposed N-terminal helix in the fusogenic state (generated by the gp120-CD4 interaction). We have dissected the e-gp41 molecule making the N-terminal and C-terminal peptide domains. Structural studies and biochemical measurements of these peptides will help gain a clearer picture of their inhibitory activity. Other functional regions of the gp41 protein have been expressed in bacteria, including the cytoplasmic domain, which is though to interact with the HIV matrix protein (a component of the nucleocapsid) as well as various host cellular factors. These are being characterized for use in NMR studies. Significance and future direction The high-resolution structure determinations of the gp41 ectodomain will allow a more rational approach to the design of novel peptide inhibitors. Based on the physical properties of the gp41, models of membrane fusion have been proposed which involve partially associated protein complexes. These models may also provide useful clues for targeting gp41. A more complete picture of membrane fusion will require more extensive structural work on gp41, especially those regions involved in mediating interaction with gp120. The expression of various engineered gp120 proteins, including the N- and C-terminal domains which are thought to interact with gp41, have been expressed and are being tested.